Dataset: Prokaryote and eukaryote abundance in phytodetrital aggregates (PA), fecal aggregates (FA), and the ambient seawater from samples collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda

Particles were collected on the monthly sampling cruises affiliated with the Bermuda Atlantic Time-series Study (BATS) in fall 2017 (AE1718) and spring 2018 (AE1809) using surface-tethered Particle Interceptor Traps deployed at 150 m, 200 m, and 300 m depths for 72 h (Table 1). To collect particles with minimal alteration to their structure, traps containing a polycarbonate jar with 100 mL of 12% polyacrylamide gel were deployed at each depth. Seawater was collected from the surface, deep chlorophyll maximum (DCM) or 20 m above the mixed layer depth (MLD), and at every trap deployment depth using 12 L Niskin bottles mounted on a CTD rosette.

8 particles were categorized and manually picked based on their morphology using characteristics described in the literature (phytodetrital aggregates or fecal aggregates), washed three times using ultrapure nuclease-free distilled water (Invitrogen), and pooled in Eppendorf LoBind tubes stored at -80C. For DNA analysis of the microbial community in the ambient seawater, 2 L from each sampling depth was filtered onto GF/F and stored in Eppendorf LoBind tubes at -80C.

DNA from the pooled particles and GF/F were extracted using a DNeasy Blood and Tissue extraction kit, and bacterial and eukaryotic paired-end V4 amplicon sequences were acquired via an Illumina MiSeq platform.

Problem report: 
As a result of low DNA yield, five samples of pooled aggregates failed PCR amplification attempts using eukaryotic (18S, V4) primers: fall 200m and 300m phytodetrital aggregates, fall 200m fecal aggregates, spring 300m phytodetrital aggregates, and spring 300m fecal aggregates.

Supplemental file "16S_Control-Blanks_Species_Raw.csv" contains the taxa excluded from downstream analyses.